refactor: mirror module namespaces to their directories (task 0031)

Adopt the convention that a Module's option path mirrors its directory
under modules/, with an index file naming the directory's own segment.

- Group agent Modules under modules.agents.*: claude-code (whole
  directory), pi (flattened to a file), skills (renamed from
  agent-skills), and gitea-axi under an agents/tools/ subgroup. The
  agents/ and tools/ folders are pure namespace prefixes with no
  aggregator enable.
- Nest hypridle and hyprlock under modules.desktop.hyprland.*, with
  hyprland.nix as the index, and update the desktop aggregator.
- Remove the obsolete example Module.
- Record the convention in CONTEXT.md and ADR 0004, and update the
  neogaia host, the two live CLAUDE.md gotchas, and the skills Module's
  intentional Enable-convention exception comment.

modules/agents/claude-code/skills/setup-skills/LOCKFILE.md

@@ -0,0 +1,53 @@
+# Skills Lockfile
+
+`.claude/skills-lock.yaml`, at the root of a project, tracks which library
+skills (from `~/.claude/skills/library/`) have been copied into that
+project's `.claude/skills/`, so [`setup-skills`](SKILL.md),
+[`update-skills`](../update-skills/SKILL.md), and
+[`remove-skills`](../remove-skills/SKILL.md) all agree on what's installed
+without re-deriving it from the filesystem.
+
+## Schema
+
+A YAML list of entries, one per installed skill:
+
+```yaml
+- name: nbdev
+  hash: 3f2a9b8c1d4e5f6a7b8c9d0e1f2a3b4c5d6e7f8a9b0c1d2e3f4a5b6c7d8e9f0a
+- name: terraform-conventions
+  hash: 9c1d4e5f6a7b8c9d0e1f2a3b4c5d6e7f8a9b0c1d2e3f4a5b6c7d8e9f0a3f2a9b
+```
+
+- `name` — matches both the skill's directory name in the library
+  (`skills/library/<name>`) and its copied directory name in the project
+  (`.claude/skills/<name>`).
+- `hash` — the output of `hash-dir.sh` run against that one skill's
+  directory contents, recorded at the moment it was last copied or
+  confirmed up to date. Never a hash of anything else — not the whole
+  project, not the whole library, just that one skill's own directory
+  tree.
+
+## What a mismatch means
+
+To classify a skill's state, compare three values: the lockfile's stored
+`hash`, `hash-dir.sh` on the project's current copy
+(`.claude/skills/<name>`), and `hash-dir.sh` on the library's current
+source (`~/.claude/skills/library/<name>`).
+
+| stored vs. project copy | stored vs. library source | meaning                              |
+|--------------------------|----------------------------|--------------------------------------|
+| match                     | match                      | nothing to do                        |
+| match                     | differs                    | library moved on — safe to update    |
+| differs                   | match                      | project customized on purpose — leave it |
+| differs                   | differs                    | conflict — report, don't touch       |
+
+## Writing to the lockfile
+
+- Adding a skill: append a new `{name, hash}` entry.
+- Applying a safe update: overwrite that entry's `hash` in place with the
+  library's current hash.
+- Removing a skill: delete its entry entirely.
+
+Never reorder or restructure existing entries beyond what an add, update,
+or remove requires — this file is meant to diff cleanly in a project's
+git history.